


Chains of Command

by amoeve



Category: Stargate Atlantis
Genre: Dom/sub, F/M, Romance, Slow Burn, Smut, Teyla and Kate definitely ship John/Elizabeth, To Be Continued, also hilarious games, some hurt/comfort later on, then more smut, will be BDSM eventually
Language: English
Status: In-Progress
Published: 2014-11-08
Updated: 2014-11-08
Packaged: 2018-02-24 14:58:43
Rating: Mature
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 4,990
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2585624
Author URL: https://archiveofourown.org/users/amoeve/pseuds/amoeve
Summary: <blockquote class="userstuff">
              <p>John pushes Elizabeth too far, so she handcuffs him to her desk to teach him a lesson. He, uh, kind of likes it, and since he's up to his eyes in denial, he doesn't quite know how to ask for more. Hilarity (read: sexual frustration, missions going wrong, no clothes, strange clothes, Teyla and Kate scheming to get them laid) ensues.</p>
            </blockquote>





	Chains of Command

**Author's Note:**

> This started as a kinky, fun little "let's look at Sheppard on his knees" fic for purposes of pure amusement, but it's grown into a 20K+ warren of plot bunnies, which are not worth publishing on AO3. Many, many thanks to my beautiful, brilliant beta and best friend of twelve years, [intentandinvention](http://archiveofourown.org/users/intentandinvention/profile), without whom the entirety of this fic would be one of the many languishing, abandoned, on my hard drive.
> 
> As it is, it’s languishing in fragments while I work out how to pull the whole damn thing together. I’m trying, I promise! 
> 
> Blame Sheppard. He’s so deep in denial that he’s looking at the Pyramids.

_“I think about Pompeii when I feel an end is near,_  
_just before the rain and every time you disappear._  
_I think about a teacup, suspended and half-served,  
_ _and all the scholars know is that it's perfectly preserved.”_

_– Dar Williams, ‘This Was Pompeii’_

 

Elizabeth is out on the balcony like she always is when she wants to think, or pull faces that might be spotted through floor-to-ceiling glass, or discipline people who want to walk away with their dignity intact. 

She doesn’t even turn around when he comes out of the doors. And then she says, “Hello, John,” in that dry tone that indicates he should have knocked before coming out, and he’s even more disgruntled because he knows that this isn’t going to be pleasant. “Can I help you with anything?” she continues, and she still hasn’t looked around.

She’s not looking out over the city, though. She’s glaring at her hands, which are gripping the rail like it’s slipping away from her, knuckles white. He wonders how long she’s been out here, and decides that he doesn’t want to ask. He settles for a shrug that she can’t possibly see. “What, can’t a guy visit his commander for a chat?” 

She turns, a little, her hands still locked around the rail. The look she shoots him scorches across his skin and he realises he’s never seen Elizabeth Weir angry. Not until now. “John. Don’t.”

“I… sorry,” he says, but that’s not the point, that’s not what he needs to apologise for. He knows it. She doesn’t say anything else, just shakes her head and looks away, and that’s when he knows he’s crossed a line he’s not sure he’ll make it back from – and that it bothers him.

A cold wind cuts across the balcony, catches what he wants to say and carries it out over Atlantis, leaves him floundering. John knows what she’s doing by not saying anything of consequence. She’s choosing to let him decide whether to face her head-on. And – he guesses from her continued silence – she’s not sure whether he even deserves the luxury of that choice.

He opens his mouth – and closes it again as he realises that she’s right on an uncomfortable number of levels. If he walks away from this conversation, he’s not sure what that will make him. He looks at her and tries not to notice how that thin red shirt is pressed against her back by the wind. She must be freezing.

He  _likes_  Elizabeth. He likes her a lot. She’s a good leader. She’s taken the time, every day since they arrived in this galaxy, to speak to at least one member of the expedition team, making sure they have what they need and are as happy as they can be. She’s a talented diplomat, solving problems with words the way he usually only manages with at least the threat of weaponry. 

It’s not even that her orders were bad. It’s just that, this time, he disagreed with her decision. And then overruled her somewhat heavy-handedly, in public, when it probably wasn’t necessary. If he’s honest with himself, someone else could have dealt with it. He just …he knows what he’s doing and he prefers to just go ahead and do it because he’d rather put that pressure on himself than assume someone else can handle it.

John swallows, rubs at his neck under his collar as if he honestly thinks it’ll help get rid of this strangling feeling. He’s surprised at how uncomfortable he feels. If he walks away from this conversation, if he takes the easy out she’s offering him, he’s not sure what that says about the chain of command on this mission. He can imagine how it will go. Oh, she’ll let him walk out. She won’t mention it again, most likely, except to keep him in line in the future. But she’ll let him know that she remembers, and that moving on for the sake of the expedition isn’t the same as forgetting. It definitely isn’t forgiving.

They’ll function as a command structure. Probably better than they do now, because he’ll toe the line more, John admits to himself. He watches another gust ruffle her curls, and suspects that he’ll obey because he’ll feel that unpleasant prickling of guilt from this devil’s bargain. He can avoid this conversation, get away with it for the sake of his command, but they’ll never be friends again. Not to mention that any respect she has for him as a person will leave with him.

Even worse, he’s not sure he’ll deserve her respect, if he leaves.

“I’m busy, John,” she says, in defiance of all the evidence. The breeze snatches at her words and he wonders whether, if it comes to shouting, anyone will hear them down below.

He braces himself. “Would this be better in your office, then?”

She turns and looks at him. She’s cultivated a spectacular poker face, he knows, throughout a very successful career, so there’s something chilling about the fact that he can see just how angry she is, and how well she’s keeping on top of it. “Very well,” she says, and if she sounds a little cool, well. Anyone else would have raised their voice by now.

A shiver goes through him as she stalks past, an animal sense that he’s in for it now.

After the wind howling around the balcony, the silence inside slices into his thoughts. By the time he’s moved around the desk and taken a seat, Elizabeth has rested her hands, palms down, on the surface. She watches him sit but stays standing, her eyes greener than he’s ever seen them as she appraises him. She doesn’t say a word. 

“Elizabeth,” he starts, and then he swallows again, because her steady stare is starting to fray his nerves.

“John,” she replies, and her eyes are as cold as the ocean below. She’s not going to offer him any help at all, he realises. He needs to drive this conversation on his own.

“Look,” he says, “I thought it was the right thing to do.”

He’s surprised when she rolls her eyes. “For goodness’ sake,” she says, impatiently. “How stupid do you think I am, Major Sheppard? You wouldn’t push so hard for something you thought was wrong, would you?”

John really doesn’t have anything to say to that.

Elizabeth shakes her head and stands up straight. “We have a problem, John,” she says, folding her arms, and she’s still looking at him. That heat gathering under his ribcage, annoyed and ashamed, starts to press on his chest. He takes a breath, but she cuts him off before he can begin. “I knew you had issues with authority when I brought you onboard. I thought you might perform better with a civilian commander. I thought that if I earned your respect, that if you trusted my judgement, this expedition would be a success.”

“I do trust you,” he says, an anger of his own burning in his belly now. “I respect your judgement, Elizabeth. And the success of this mission doesn’t rest on my ability to listen to you – don’t you pin that on me.”

“Doesn’t it?” she snarls, the mask of calm dropping abruptly. “Doesn’t it, John? When you’re undermining my authority and your men follow your orders rather than mine, wouldn’t you say that this expedition is in trouble? Because you can’t have it both ways, Major! You can’t play the flyboy and go off on missions and leave me to manage this city, and then expect to come home and take over the reins every time you disagree with a decision that I have made!” 

“That’s not what I – ”

“ _Don’t you dare_ ,” she says, and he’s cut off as surely as if she’s put a hand over his mouth. She leans forward again, and he definitely doesn’t lean back. “Don’t you even think about interrupting me until I am finished, John Sheppard. You’ve had quite enough say for one day.” And she pauses, then, and he knows in his bones that she’s testing him.

He raises his hands, keeps his mouth shut.

“ _Thank_  you,” she says, with an almost offensive level of grace. “How many crates of rice do we have in the city at the moment, Major Sheppard?” she asks, so sweetly that he is completely thrown. “Any idea?” She pauses as if to let him speak, but when she glares at him he’s not so sure that’s a good idea.  He doesn’t like the doubt burrowing its way under his skin.

“How many personnel have signed up to the educational programme for the Athosian children on the mainland?” she continues, relentless. “How many rest days are scheduled for offworld teams between missions, and who ensures that they don’t overlap with the teaching teams?” she adds as she stalks around the desk. She leans over him for a moment, too close, and to his surprise he feels two fingers press under his chin, push his head up. He thinks for a moment that she’s trying to look him in the eye, but then realises she’s examining the cut on his forehead. He tries very hard not to shiver. He tries to keep his gaze fixed on her eyes. “How about stock levels of antibiotics, John?” She pulls away, moves around behind him, and she’s too close for him to be able to spin the chair to keep her in his line of sight so he stares at the wall instead because he refuses to crane his neck to look at her. “Or the rota of assignments to the canteen and the laundry? Or because you were excused auxiliary duty as the military commander of this city,  _Major_ , did you even bother to notice that someone has to organise all of this?”

“I don’t want to run the city, Elizabeth!” he manages in the ringing silence. She rests her hands on his shoulders and he freezes, feeling it right down his spine. Her hands are cold where they overlap his collar, one thumb just brushing the skin at the nape of his neck.

“I know you don’t,” she says, very softly. “John, you’d be a terrible administrator. You’re very, very good at what you do,” she says, lifting her hands from his shoulders. “But you’re reckless, and… as much as I regret saying this because you’ll wilfully take it the wrong way, you’re irreplaceable.”

For a moment he’s back in familiar territory. “Well, thanks, but I hardly see what that has to do with my –  ”

He feels the faint touch of her hair brushing his head as she leans over his shoulder again. “I said it the first day we were here, John. Someone needs to think of the consequences.”

It takes him a moment to really hear the soft click, to feel the chill of metal slip around his wrist. Elizabeth stands up and moves into his field of view, and he tugs instinctively with his right arm, but all it does is make his wrist throb in pain and shift the wheeled chair closer to the desk.

It takes him far longer than he likes to process that she’s  _handcuffed him to the fucking desk_.

“Elizabeth,” he snaps, and he’s lost for words for a few moments because this is so far away from anything he was expecting from Elizabeth Weir that he has no idea how he’s meant to react. Finally, the appropriate spark fires in his brain, and he turns the chair to her, which pulls his right arm out straight. “What the hell are you doing?” He’s already seen that the table is fixed to the floor, probably because the Ancients built their bloody city to be able to fly. There’s no way out of this except with the key that – he looks up, and she’s re-doing her necklace, the little silver key resting next to the charm she never takes off. “The hell is  _this_?” he clarifies, tugging again at the cuff in disbelief.

“Oh, stop that, you’ll hurt yourself.” She folds her arms and he stops, if only because the edge of the cuff is starting to dig into his wrist. “I’m sorry it came to this, John,” she says, all calm again. “But I have to teach you a lesson somehow.”

Teach him a …? “You’ve  _handcuffed_  me to your damn  _desk_ ,” he protests. “What exactly are you trying to teach me?” 

She leans down until her face is level with his and closes her fingers over the cuff. He flinches, and her other hand grabs his left arm as he lifts it instinctively, defensive. Her grip tingles against his wrists; her hands are still so cold. The hair rises on his arms, on his neck, all the way down his back. Her eyes are so bright, afire, and he’s alarmed to see something mischievous glinting underneath that anger and determination. He takes a breath and – just has no idea what to say.

Her face is inches from his. If he so much as moves, he’ll headbutt her. Or something. He swallows. “So I might have taken ‘chain of command’ figuratively,” she says, but she doesn’t sound amused, or like this is a joke. “But something was needed to shock you out of your comfort zone. John… I need you to learn to listen to me.” He feels a sick rush of horror at just how  _disappointed_  she sounds. “Please. For your sake, and for the sake of this expedition. We’re a long way from home out here, and I need to be able to trust you – and I would really like for you to trust my judgement, too.”

“Elizabeth,” he manages, because this is madness, she’s cuffed him to the desk, he’s the ranking military officer and her office is glass-fronted and she’s still looking at him as if she’s searching for something, and she’s closer than any woman has been to him for quite some time –

She steps back, expression unreadable, and strides out of her office.

“Elizabeth!”

The doors slide closed behind her. He watches her walk away, and abruptly realises that everyone can see him too. Sitting here, waiting for her to come back. John shivers, gooseflesh prickling under the cotton clinging to his skin. 

He has to grant it to her, he thinks sourly, looking down at his wrist, at the silver link around the leg of the desk. He definitely didn’t see this one coming.

 

*

 

It’s dawning on him a few minutes later that she’s actually just left him here. Cuffed to her desk. Cuffed to her desk, in fact, with piles of paperwork and nothing else to look at. Oh, he twists around a couple of times – all right, a few times a minute – to see if he can see her coming back, or to see anything at all. The team in the Control room beavering away with new tech, maybe, or staff passing through the gateroom on their way elsewhere.

It’s too quiet in here. The bustle of the city is reduced to a bothersome hum, hovering just on the edge of hearing.

John Sheppard is sweating.

He turns again, catches one of the Control staff looking at him and feels a hot spike of something close to alarm.  _What if they see?_  he thinks, but he raises his free hand and smiles nonchalantly. Then he turns back fully to Elizabeth’s desk, heart thumping in his chest, and lifts up some of her paperwork to see if he can find anything useful in there – an excuse for being here at the very least, in case someone comes in, because if word gets out that he let Weir cuff him to her desk, he’s done for. Ford won’t let him live it down. Bates won’t listen to him ever again.

The thought bites into him, gently, like the metal against the soft underside of his wrist. He can imagine what they’d say. God, he can imagine it in their reports to Stargate Command when they get back. If they get back.  _After he questioned the chain of command, Dr. Weir cuffed the Major to her desk and left him there until he got the message_. They’d either laugh themselves sick or discharge him on the spot.

He imagines the look on O’Neill’s face and barely manages to suppress a groan.

He freezes in horror as he hears the door slide open. He hopes, by all that’s holy and he doesn’t believe in, that whoever it is didn’t hear him through the glass. He schools his face into what he hopes is an expression of mild interest and turns his head to look at almost the last person he wants to see right now: the world’s most offensive Canadian, with a touchpad in his hand that will hopefully hold his attention enough to make him even less observant than usual. McKay looks up when John turns, as if he’s not quite registered where he is, and raises an eyebrow at Elizabeth’s empty chair. 

“She’s just left you here, then?” the scientist chuckles. John makes a point of shuffling some papers and absolutely not checking that the cuff on his wrist is concealed. His pulse is thumping in his chest, sudden, something unutterable flooding through his veins, Elizabeth’s name stilling on his lips as he realises that he wants to see her face, wants to watch her take this in and see what she’d decide to do next.

“Uh… apparently something urgent came up,” he improvises, hoping McKay doesn’t ask why he isn’t using his right hand, his writing hand, or why he let that pause go on just a few seconds too long. “I guess I’m just not a priority.”

“You said it, not me,” McKay smirks, safe in the knowledge that Weir isn’t going to be shouting at him today. “Do you know where she went? I want to go over the preliminary lab reports with her.”

John decides it's appropriate to glare. "If I knew where she was, do you think I’d be sitting here waiting?"

Rodney shrugs. "She might have ordered you to wait."

“Because obviously I would have nothing better to do.” He ladles on the sarcasm on that one, but goddamn Rodney just starts to laugh.

“Oh, boy, she did, didn’t she? She’s actually making you wait for her, just to make a point.”

John decides that discretion is the better part of valor, and focuses his attention on the paper he’s picked up at random, ignoring the hammer of his pulse. It’s the fifth page of a report on chemicals extracted from some plants found on the mainland, and whether they can be adapted into drugs useable in the infirmary in case the exploration teams use up all the meds they have in stock before they manage to trade for more (or make some way of connecting to Earth, thus solving all of their problems).  _Likely we will need to be self-sufficient if consumption continues at current rate_ , he sees in Elizabeth’s neat cursive.  _Please notify me as soon as we have less than twelve weeks’ supply_. He’s starting to feel guilty for gallivanting offworld and leaving Elizabeth to worry about painkillers and antibiotics when McKay speaks again.

“Look, far be it for me to say it’s all your fault, Major, but it really is. Besides, you wouldn’t even be here without her,” he adds. “The rest of us had to get through months of evaluations and fitness tests. You got a ride all the way to the top because she wanted you for this expedition. And then you contradicted a direct order, putting the entire base in danger, so she’s going to make you so sorry for it that – metaphorically speaking, of course – you won’t be able to sit down for a week.”

Trust McKay to sound resentful when he’s putting someone in their place, John reflects darkly. “Are you done gloating now?”

McKay beams at him, far happier than he has any right to look. “Absolutely not. But I have a fascinating experiment running and I don’t want Zelenka deciding to let those amateurs get their sticky hands all over it in the name of education. If I see Elizabeth,” he adds over his shoulder as he heads out the door, “I  _might_  mention that I saw you waiting like a good boy.” 

That stings, and John grabs the first thing that comes to hand – a heavy metal paperweight – and throws it, just to see McKay back up a step. It hits the glass with a dull thud, but his luck has definitely run dry today;  Rodney just waves to him gleefully and disappears out of sight.

John turns back to Elizabeth’s desk and assesses the mess he’s left. He realises guiltily that he’s not going to be able to retrieve the paperweight, and also that she might actually want it for its intended purpose. He’s sure her papers were more in order before, although in his defence he wasn’t the one who decided he needed to be handcuffed to her desk.

It’s still not quite sinking in. His wrist twinges against the metal. John glares down at it. “Traitor,” he says, and he doesn’t care that he’s being ridiculous. His wrist doesn’t need to be on Elizabeth’s side, too.

Still, it can’t hurt his case to not leave her desk looking like a bomb’s hit it, so he starts to sort through the piles he can reach, but he can’t tell where one report ends and the next begins. And then he sees that his personnel file is lying open on the far corner of the desk, underneath a couple of sheets of paper with McKay’s drunken-spider scrawl all across them.

That’s when he realises that this might actually be more than just a way to psyche him into doing what Elizabeth wants.

He risks a glance over his shoulder and decides that he  _has_  to see that file. Rodney’s long gone and nobody’s paying attention to him anyway – they just think he’s waiting for Dr Weir to come back. He shimmies the cuff up as high as it will go on the desk’s leg, and braces his wrist against it.  _Screw it_ , he thinks, and stands. He can’t make it all the way to upright, but he can reach across the desk – uncomfortably splayed, all right, but anyone watching won’t notice he’s not just being too lazy to stand all the way –

Behind him, the doors open and he moves hurriedly back to sit, but he hears, “Looking for a little light reading to pass the time?” as Elizabeth pulls the chair away. He loses his balance and falls forward onto the desk, barely bracing himself on the hand that was reaching for his file. He feels his face flush as he realises what he must look like. He hears her step up behind him, oh God, he can feel how close she is – and her hand comes down on the back of his neck, warm and gentle, pressing him against the desk.

His whole body is tingling. He feels almost delirious, a thrill of something very close to humiliation.  _Anyone_  could look around and see them like this, see her pressed up against him, see him bent over her desk. “Oh, John,” she says, so gently that his legs tremble. “And you were doing so well.” 

He’s spread-eagled on her desk with his face pressing into a pile of paper. He can’t seem to catch his breath, and heat is spreading from his chest outwards, down. His back aches from the angle and he trembles again when she runs her fingers through the hair on the back of his head. Nerve endings flare, from the nape of his neck all the way down to his balls. John closes his eyes, swallows hard. His head reels. He can’t believe Elizabeth is…  _what is she thinking?_

He’s never been so turned on in his _life_. 

“Anything I can help you with, Major?” he hears her say, sweet as anything, and oh, suddenly he can think of a  _lot_  of things – and then she’s gone again. For a second he finds himself missing the firm pressure of her hand on his neck, and he shivers, opening his eyes. She slides into the right-hand edge of his peripheral vision on the chair she pulled away from him, undoing her necklace.

“There is this one thing, Elizabeth, yes,” he grates, and she laughs as she unlocks the cuffs. He stands up, massaging his lower back, and he can’t quite make his eyes meet hers but he can see her arched eyebrows and he really bloody hopes  _her_  eyes stay above his waist. He makes a show of adjusting his jacket, smoothing up his collar, and when her gaze lingers on the mess he’s made of her desk he adjusts elsewhere, more subtly than he’s ever managed to before.

“Will that be all?” She stands up, looking frustratingly innocent – and then her eyes slide past him to the control room. He whirls around, worried that someone’s  _seen_ , and blood rushes to his head. He stumbles – but she’s already there. She steadies him, one arm slender and strong around his shoulders. Nobody is looking at them, to his endless relief, but Elizabeth’s renewed presence in his personal space really isn’t helping his… situation.

“Are you all right?” 

He glances down at her in confusion, but there’s no mockery there. She appears to be genuinely concerned, her eyes and tone gentle, but there’s still something sparkling there that he doesn’t quite know how to place. “I’m fine. Honestly,” he says, pulling away. He spots the paperweight on the floor, and tries very hard not to think about the weight of her hand on his neck as he bends to pick it up.

When he turns to hand it to her, he sees that she’s folded her arms. “Was there something you wanted to say, Major Sheppard?” She sounds perfectly serious, but she looks far too composed for his comfort. He’s so hard it hurts. He seriously thinks there might be something wrong with him.

“I... uh… I reckon you’ve given me a lot to think about.” It’s a pretty graceless sentence, he’ll be the first to admit, but there’s no need for her to look so damn smug.

“I’ll let you get on with it, then.”

She smiles at him brilliantly, and he makes for the door. He stops in the doorway and looks back at her, sure that he should have something to say. He really shouldn’t be thinking she looks beautiful when she’s got the upper hand.

He doesn’t want to think about her hands, or where the upper hand might go. John decides he might just retain what little dignity is left to him if he leaves, so he does.

 

*

 

He doesn’t even try to go about his day as he usually would. Generally, after a mission and the inevitable meetings, he’ll get some food, have a nap, and then see who’s free to hang out for a drink and some downtime. As he moves through the hallways of Atlantis, he finds himself nodding briskly to people and moving on as if he’s busy. He can’t stop touching the back of his neck, feeling where Elizabeth held him down. It’s like she imprinted something sizzling onto his skin, and he can’t think straight because he liked it, he  _really_  liked it, and he wants to feel it again. Perhaps not with his professional image on the line, and the possibility that someone else might see him bent over Elizabeth’s desk.

No. No, actually, even that’s thrilling, every nerve trilling an agonised desire to have her show him his place.

John stops, feeling hot all over – and sees someone notice he’s broken the flow of personnel in the corridor. Cadman, the prettiest bomb-disposal expert in the galaxy, and now he’s caught her eye. “You okay, sir?”

“Yeah, fine – just realised something I forgot to do.” He flashes her a grin and quickens his pace, feeling as if every hair on his body is up and quivering. Something else is up and quivering too, and he’s really trying not to think about that. As soon as he’s out of the main thoroughfare, he ducks around a corner and starts running, avoiding the residential floors and the areas marked for exploration this week, pushing himself, punishing, hoping like hell that nothing comes over the radio because he is in no state to respond to a crisis.

Getting worked up and warm might give him another kind of rush, something to tire him out, to replace the tingling desire to go back to Elizabeth’s office and get on his knees and beg her to let him come.

He runs ten kilometres before he makes it back to his room. He doesn’t even stand there panting, checking his performance like he usually does – he peels off his clothes and steps over them, heading straight for the shower. Until now, he’s never regretted bribing McKay to re-jig the settings so the jets are strong enough to beat tension out of his muscles, but when he tilts his head back under the water and the pressure of it on the back of his neck has him whimpering, he can’t stand it any more.

John takes himself in hand and tells himself he’s not going to think about the gentle firmness of Elizabeth’s palm holding him in place, her fingertips teasing against the hair on his nape, his face pressed into piles of paper, the pressure of her thighs against him from behind… he’s never been so confused in his life.

 _You were doing so well_ , he remembers, oh God he remembers, and he comes so hard that he can’t breathe and for a while he forgets his own name.


End file.
